Nine days during the Beginning
by SuOmAlAiNeN92
Summary: Prequel to my first two stories. During the Last Great Time War, a Dalek weapon, thought destroyed, was cast to Earth. The plant life there grew to become deadly when their fumes were breathed and are dangerous in wrong hands. Newly regenerated Ninth Doctor seeks to find and destroy this weapon. Even if he has to face the Gotham underworld, as the Batman begins his war on crime.
1. Flowers

**Author's notes: **For the sake of _Batman: Arkham Origins _being a prequel to two first games, I decided to make a prequel to my two first stories. This takes place during _Batman Begins _and before _Rose, _so this will be a Ninth Doctor story. Also, I believe you'll be happy/sad/furious/have mixed feelings on who his companion will be.

* * *

**Flowers**

It was almost dark in mountains of Himalayas. A great monastery that had once been a training facility for centuries old organization, the League of Shadows, had been burned and was now nothing but ruins of burnt wood and ashes. Some ninjas had escaped and a traitor who had set their home on fire. Only one who the traitor had saved was his teacher. The man, who had saved him from a cell and given him a path to follow, a path he had decided not to walk to its end.

In front of the ruins stood another man, not dressed for the coming coldness. He had followed his own path there. Not a path led to him, but a path he saw his responsibility to follow, not caring what he would find at the end for himself.

Reaching to the pocket of his black leather jacket, this man pulled out as small blue torch, which made whirring noise as he waved it across the ruins in front of him. Looking at his torch after words, he seemed at first content to the results,

''Good riddance,'' the man said, before seeing that there was only a small partition of what he was looking for. The trail he had followed to the ruins was still on going, and by now what he was looking for could have been anywhere.

''Fantastic,'' the man said in annoyed and sarcastic tone in his voice.

His work here was far from over. Bitter with his findings, the man turned away from the ruins and returned to his Police Box waiting for him few feet away. As he stepped inside and let the door close, the Police Box began to fade out of the scenery.

* * *

The TARDIS returned to existence at a small airport further away from the mountains. The Doctor stepped out and closed its doors, locking them. Then he walked to customs office and pressed bell desk, letting the workers know he needed service.

''Coming, coming,'' a young brunette girl wearing a TSA-jacket said coming to the desk behind a curtain, ''how can I help you?''

''I would like ask some questions,'' the Doctor said showing black leather bound wallet, or the psychic paper, with his credentials to the TSA girl. ''In the last few days, have you been letting any huge shipments come through your airport and out of the country?''

''What kind of shipments?'' the TSA girl asked.

''Big ones,'' the Doctor said pulling as small blue flower from his jacket, ''carrying these.''

The TSA girl took a look at the flower, but didn't seem to understand what it was.

''I don't actually know if there has been, I'm going to have to ask my supervisor,'' was the TSA girl's response.

''Fantastic,'' the Doctor said in a monotone voice as another man came out behind the curtain.

''I heard everything this man asked you and you really have to do better customer service,'' the other TSA agent said and pointed the TSA girl to get back behind the curtain.

''I wasn't complaining her service, so you don't need to rude to her,'' the Doctor said defending the TSA girl, before showing his credentials to the male TSA agent. ''Doctor John Smith, UNIT, I would like to know if there has been any shipments coming through your airport past these few weeks, carrying particularly any of these?''

The Doctor threw the blue flower to the reception desk and the TSA agent took it for examination.

''What exactly is this?''

''It is flower that has been growing on a ground in the mountains, that has been radiated with an unknown radiation from a solar storm not many but enough centuries ago that it has been evolved to stage that its fumes can cause a deadly reaction to human psyche if inhaled too big of dose.''

The TSA agent looked back to the Doctor with a blank face.

"What?''

The Doctor shook his head.

''Just tell me if there has been any shipments and it there has been, where had they gone to?''

''There has not been any,'' the TSA agent said calmly.

''Aren't you even going to look throw your manifests?''

''There has not been any shipments going through our airport.''

''But-''

''There has not-''

''Fine,'' the Doctor said taking the blue flower back and turned to the exit. ''Thank's for nothing.''

* * *

The Doctor had already walked out the doors and was heading back to the TARDIS when he heard a scream.

''LOOK OUT!''

He turned back and saw the TSA agent pointing a gun at him, but was surprised from behind by the TSA girl. She jumped on her supervisor and gave the Doctor a chance to repay her warning with a kick to the TSA agent's stomach and a knockout punch behind the back of the head.

''Thank you, for actually doing anything here,'' the Doctor said pulling the girl up on her feet and turned back to his TARDIS.

''Are you just gonna leave?'' the TSA girl asked.

''Yup.''

''Just like that?''

''Yup.''

''Can I come too?''

The Doctor turned back to the TSA girl, watching her with calm and sore eyes.

''You saved my life, I helped you out of it'' he said and resumed to walk away. ''We're even, so no.''

''I know where those flowers are going!'' the TSA girl said and the Doctor stopped. ''Take me with you and I'll tell you where.''

The Doctor walked back to the TSA girl and looked at her bitterly.

''Why would you want to come with me?''

''I just watched my boss, who didn't really like that much or this whole place, try to kill someone,'' the TSA girl said, almost laughing at the obvious reason. ''Anywhere else but here is fine to me.''

The Doctor was about to say something but as he saw the homicidal TSA agent regaining consciousness, he grabbed the TSA girl's arm and said: ''Run!''

And they ran, to the TARDIS.

''Why are you opening that box and where did it even come here?'' the TSA girl said as the Doctor put the key to the keyhole in the door.

''This is as much as a box as your boss was telling the truth,'' the Doctor said opening the doors and pulled the TSA girl in with him. ''Don't worry, even armies of Tsingis Khan can't open those doors. And believe me, they've tried.''

The TSA girl looked around the room inside the TARDIS, with her reaction being pretty much the same as other humans who had entered it.

''Yes, it is bigger on the inside, lets skip that part and focus on where those blue flowers are going!'' the Doctor said standing in front of the console, facing the TSA girl. ''Well?''

It took a few seconds for the TSA girl to regain her thoughts and answer.

''Gotham City. There was a man who came from the mountains with one of those flowers in his clothes and called a plane for himself from Gotham City.''

The Doctor stood silently thinking. One flower might have been a little sample, which when synthesized could have been manufactured to bigger amounts. Not maybe as powerful as the ones grown in the radiated ground, but enough to cause trouble.

''Gotham City,'' the Doctor said turning to the console and began to turn switches, pull levers and press buttons. ''That's a start.''

As the course had been set, the Doctor turned to the TSA girl.

''I'm the Doctor, by the way. What's your name?''

''Clarissa Oswin, or just Clara for short.''

* * *

**Author's notes: **And this is the part where I usually ask you to review. So basically, REVIEW.

Also, as you saw, the Doctor is a bit surly, bitter and not very happy. This is because he has just lived through the Time War and just recently regenerated from John Hurt to Christopher Eccleston. Rose has not yet met him and made him the better person Tenth Doctor credited her for doing.

I would also like to say that I am not sure how often I am going to update this. I just started an internship in an 8 hours per day job and I'm also trying to write that book I mentioned in my profile. But when ever I can, this story will go on forward.


	2. Eavesdrobbing

**Author's notes: **For those who read the last chapter and were shocked by the identity of the Ninth Doctor's companion's identity, yes she is one of Clara Oswald's echoes. I am pursuing to write her to act as the Clara we know, but to seem like a different person, so that when the people who have survived to _The Dark Knight And The Doctor _won't recognize her as the same person. And also the Doctor first consciously met Clara in the Dalek Asylum, where he was 300 years older than here. Basically connecting the dots from a memory that far ago would make this Clara-echo, or Clarissa, a total OC who could be connected to Clara only by the little, unnoticeable things.

* * *

**Eavesdropping**

The TARDIS landed to an alley between buildings. The Doctor took a glance at his new companion and caught her about just walk out the doors.

''Oy! Where do you think you're going!?''

''Outside, you said we'd have moved from the mountains to America,'' Clarissa answered stopping what she was about to do. ''I wanna see it.''

''Dressed like that?'' the Doctor said pointing at her TSA uniform. ''We're miles away from any airports, people are gonna ask questions.''

''Oh,'' Clarissa said looking at her cloths.

''There is wardrobe through there,'' the Doctor told Clarissa pointing to a door way out of the console-room. ''First left, second right, third on the right, go straight ahead, under the stairs, pass the bins, fifth door on your right.''

''Are you gonna change?'' Clarissa asked walking past the Doctor. ''I mean, a waist-coat with leather jacket is a bit…''

The Doctor looked down his clothes and snorted. He threw the leatherjacket to one of the chairs around the console, loosed the waist-coat and put the leather jacket back on.

''I'll change the jumper later,'' he said walking back to the doors and looked out. ''If I'm not back by the end of your private fashion show, find me from that building we're across from.''

* * *

The Doctor stepped out and pointed his sonic screwdriver at the lock, locking it from anyone else but him to open. Thought Clarissa could come out when she was ready, she'd need him to get back inside. The Doctor walked across the street, to the city hall. He assumed that if the flowers had arrived to Gotham, there ought to be something about them in public records. If that effort were to turn out un-fruitful, he could always eavesdrop on people.

As the Doctor crossed the street, he bumped in to a man whose face was covered in the shadows under his hood and cap. Neither man said anything to each other, to apologize or to pick up a fight. They just shrugged off and walked away, the hooded man to a phone booth and the Doctor inside the city hall.

"Doctor Crane!'' the Doctor heard a woman's voice calling out and saw a woman in public servant's clothes approaching a man in grey blue suit, a sweater and thin, white rimmed glasses.

''Aw, Ms. Dawes,'' Dr. Crane said, keeping himself walking with Ms. Dawes following him.

''How is it that a man who butchers people for mob, doesn't belong to a jail?'' Ms. Dawes asked, while the Doctor twitched at her question and the fact there was such a man like that not sent to prison.

''Well, I might have testified against that if that were the case, Ms. Dawes'' Dr. Crane replied, walking and not even looking at her.

''This is the third of Falcone's thugs you have declared insane and moved in to your asylum,'' Ms. Dawes said stopping him from walking and the conversation carried on as they stood and the Doctor listened.

''Well, I have worked often on organized crime, must have grown an affection on the insane,'' Dr. Crane said and pursued to keep on going.

''Or the corrupt,'' Ms. Dawes shot back and Dr. Crane stopped again.

But instead of beginning an argument, he looked across the hall and called out some one.

''Mr. Finch! I think you should check with Ms. Dawes here, what implications your office authorizes her to make,'' Dr. Crane said calmly as another man in a suit came by. ''If any.''

The Doctor watched between Ms. Dawes and the approaching Mr. Finch, and assumed they we're the Assistant District Attorney and the District Attorney. Comparing his own clothes to theirs, the Doctor decided that if he was ever gonna wear a suit it would be too soon.

''What are you doing, Rachel?'' Mr. Finch asked his assistant as Dr. Crane walked away.

''What are you doing, Carl?'' Ms. Dawes asked back, making the Doctor question their first name bases.

''Looking out for you,'' Mr. Finch said pulling her aside, outside the Doctor hearing area.

The Doctor shook his head and look outside. The hooded man was still there looking to the city hall from the open phone booths. At first the Doctor assumed he was looking at him, but soon realized he was looking at Ms. Dawes, giving Mr. Finch a kiss on the cheek. Office romance, the Doctor assumed and looking back to the hooded man, he saw him turning away, leaving.

Not trying to understand what kind of love triangle was going on, the Doctor walked to a corridor in the city hall, where the signs said the public records were. On his way he overheard another conversation.

''No more favors,'' a voice the Doctor recognized as Dr. Crane, coming from an office.

''Hey, hey, you scratch my back I scratch yours,'' another voice said, with American-Italian accent. ''I bring you the shipments.''

''Shipments?'' the Doctor replied shocked. Taking interest in the conversation, he pulled a stethoscope from his pocket and started to listen in.

''We pay you for that,'' Dr. Crane's voice said.

''Yeah well maybe I want more than just money,'' American-Italian said.

''I know more than well that you're not intimidated by me, Mr. Falcone,'' Dr. Crane said, naming who he was talking to and the Doctor was shocked to hear Crane was talking to the man whose thugs he had been bailing out. ''But you know who I'm working for, and when he gets here-''

''He!? He's coming to Gotham?'' Mr. Falcone said surprised.

''Yes he is,'' Dr. Crane continued, ''and when he gets here, he is not gonna want to hear how you have been endangering our operation, just to get your thugs out of a little jail time.''

''So what do you want?'' Falcone asked after a short silence.

''There's a girl in the DA's office,'' Dr. Crane said, reminding the Doctor of Ms. Dawes and her previous attack on him about the murderous thug.

''We can bribe her,'' Falcone said, to which the Doctor shook his head. There was no way that woman was going to be bribed.

''Not this one,'' Dr. Crane said, agreeing with the Doctor.

''An idealist, ha,'' Mr. Falcone replied, ''we have our ways for that.''

''I don't wanna know,'' Dr. Crane said.

''And neither do I,'' the Doctor said pulling the stethoscope off and put it back to his pockets as he walked away.

No need for public records, eavesdropping had proven to be much more reliable. The flowers were coming to Gotham through Mr. Falcone and he was bringing them to Dr. Crane, but for what? What we're they going to do with the infected flowers? If they were planning to use them for drug market, that would have been a very bad idea. With them already infected with the Daleks' weapon from the Time War, drug dealers would eventually run out of customers, which would have been a good thing, if they wouldn't be dead.

* * *

Standing outside city hall next to the TARDIS, the Doctor watched as Mr. Falcone walked out. To find the flowers, the Time Lord had to follow the mobster to them and make sure they were all destroyed. Clarissa was still changing clothes, which was understandable when considered the size of the TARDIS's wardrobe. But she had better hurry up if they were to shadow Mr. Falcone.

''About time,'' the Doctor said as Clarissa came out and he turned to look at her. ''Blimey!''

Clarissa was wearing some of his previous companions' old clothes. She had Ace's old jacket, Peri's skirt with Susan's shirt and Mel's boots with some stockings. She had even put her hair like Ace had.

''Not too much?'' Clarissa asked smiling and posing like a model.

''Fine,'' The Doctor said, ''considering.''

''Considering what?'' Clarissa asked bothered from criticism.

''That you're human,'' the Doctor said turning back to watch Mr. Falcone. ''Come on, we have a mobster to follow.''

* * *

Mr. Falcone walked some blocks to a small bar and sat down to a table. The Doctor and Clarissa followed him there and took a table from a considerable length from the mobster. They also ordered some burgers not to seem strange just by sitting there. On their way there, the Doctor had used his sonic screwdriver to bluejack Mr. Falcone's mobile, and so listened to his calls. At the bar they were now, he was supposed to meet with someone named Flass.

''What is it that you're so interested about those flowers?'' Clarissa asked while they waited for Mr. Falcone's guest to arrive.

''Long story,'' the Doctor replied.

''We have time.''

''It's complicated.''

''You can tell me.''

''Really complicated.''

''I'm not stupid!'' Clarissa said, not too loud but enough to point that she was annoyed with the Doctor's behavior.

The Doctor turned to face Clarissa, who looked like hybrid of his past companions, with her only individual look being her face, which was now mixed with anger, curiosity and some sort of sympathy. Also, what she looked like, reminded him of the time before his previous incarnation and the life before he was the last of his kind.

''I'm an alien from another planet,'' the Doctor said in a sad, deep voice that couldn't be heard from other tables, which were pretty much empty. ''A planet, that no longer exists. I'm the last of my people.''

''What happened?'' Clarissa asked, believing him and showing more sympathy.

''There was a war, the Last Great Time War. The final battle between my people and another race that wanted to destroy everything that wasn't like them. In the end both sides destroyed each other, but during the war, the Daleks', our enemies dropped a weapon to Earth.''

The Doctor pulled out the blue flower he had shown Clarissa in Himalayas.

''It fell to the exact spot where these are growing and during all the years, decades and centuries, they have evolved to become a kind of psychotic when they are smelled or worse, inhaled.''

The Doctor put the flower back into his pocket.

''That's why I have to find them and destroy them, before they can do any damage to the people of your planet. I'm the only survivor of that war, it is my responsibility to make sure it won't affect a third party.''

Clarissa looked at the Doctor's mourning face, probably trying to think of something to say to him, to comfort him. Before she could, the Doctor saw a fat man with greased and curly hair and unsanitary clothes approaching and sitting into Mr. Falcone's table. As he sat down, the Doctor caught a glance of a police badge in his belt. This must have been Flass, who apparently was a dirty cop.

''I need you at the docs, Wednesday,'' Mr. Falcone's voice said in headphones the Doctor and Clarissa were wearing linked to the sonic.

''You expecting trouble?'' Flass' relaxed voice asked, before the headphones started to give static.

''What happened?'' Clarissa asked as the Doctor gave the sonic a few taps against the table. ''Okay, it's back now.''

''I heard you were having some trouble with the DA's office,'' Flass said, ''and I heard that if someone were to take care of it, they would be… well paid off.''

''What's your point?'' Mr. Falcone asked with annoyance echoing from his voice.

''Have you even seen the girl?'' Flass asked relaxed and the pupils in the Doctor's eyes grew from shock. ''I mean, don't you think taking out some her would be… too much?''

''They are going to kill the Assistant DA,'' the Doctor whispered to Clarissa.

''Never underestimate Gotham City,'' Mr. Falcone said, with his voice turning cynical and evil. ''People getting robbed, every day of the week. Sometimes… things just go bad.''

* * *

**Author's notes: **Small cameos from Bruce Wayne, who the Doctor didn't recognize. Also these scenes here, I'm not sure if thy happened in the movie during the same day, but during all of them, Bruce was dressed as a drifter.

That how I wrote Clara, or Clarissa, here, I based on how she appeared as echoes in the Doctor's timeline in different clothes and the clothes she wears are supposed to make her look like Ninth Doctor's sidekick, with black and some dark colored clothes. Or like she was shown trying to save/warn the Seventh Doctor in _The Name Of The Doctor_, where she had pretty much dressed up like Ace.

As for now... REVIEW... CREATIVELY! And next will be some time killing before the Batman makes his first appearance at the docs. Or mayby that happens right away. Time is not the Doctor's boss.


	3. Jumper

**Author's notes:** Now as I told in the last chapter, I am not 100 % sure if the timings go right in this story with the events of the film. They may or they may not, but this story will be set during as the name suggests, nine days during Batman's first days. From where we are to the League of Shadows attacking Gotham and be told from the Ninth Doctor's, ad some times Clarissa's, point of view.

* * *

**Jumper**

The Doctor and Clarissa returned to the TARDIS to think what to do next. For one, the flowers were coming to Gotham through the docks brought by Carmine Falcone, next shipment by Wednesday, meaning there was going to be a lot of Falcone's thugs between them and the Doctor. Not only would have it been a problem to get to them and make sure they were the same flowers or even flowers at all.

Another order of business was that they knew that Falcone had put a hit on Assistant District Attorney Rachel Dawes. She was, as the Doctor had observed, a driven woman and determined to fight against the corrupted system that was Gotham City. Her murder was assumed to happen in the next few days, possibly when the next shipment was going to arrive. Any sooner would have put Falcone under observation as a suspect and endangered the shipments as Dawes had actively working against the mobster.

''Even with the TARDIS, I can't be in two places at once,'' the Doctor said leaning to the console.

''What do you mean?'' Clarissa asked, making the Doctor raise his head.

''Oh, forgot to tell you,'' the Doctor said grinning proudly, ''she's also a time-machine.''

''Ah, okay,'' Clarissa said, letting the idea sink in. ''Why can't we use your time-machine to go to future and see how to save Dawes and stop the flowers?''

''Because every time I land the TARDIS somewhere, she becomes a part of the events,'' the Doctor said seriously, meaning to return to the topic at hand.

''Right, you suppose we should shadow Ms. Dawes and save her once the attempt on her life arises?'' Clarissa asked.

''We'd have to split up for that,'' the Doctor said shaking his head, ''and it's not safe going out alone in this city, especially with Assistant DA's work hours.''

''You're right, that is a risk'' Clarissa said in a thinking posture. ''What if we get involved with Dawes as in… getting friends with her? That way other one of us could be with her most of the time and-''

''And I'm sure you'd pull it off fantastically in the short time we have,'' the Doctor said putting his hands on Clarissa's shoulders. ''Unfortunately, I can't guarantee that you'll live through it, or that I'll be able to live with myself letting you go as collateral.''

''Aw, that's sweet'' Clarissa said as the Doctor let go and walked past her. ''So what do you suggest that we do?''

The Doctor walked back to the console and pull out a screen from rotating railing above it. He pressed some buttons on the console, bringing the files of Arnold Flass, the dirty cop they had witnessed Falcone meeting with. Instead of reading them through, the Doctor skipped most the file and pointed out his partner.

''Sergeant James Norrington Gordon, been in the force for twenty years, married, has two children, a boy and a girl,'' the Doctor read from Flass' partner's file. ''I first need to see him before I can assume we can trust him.''

* * *

The TARDIS moved herself from the City Hall to building between Gotham Police Department and the one next to it. It was nightfall as they landed. The Doctor kept her in the alley, to hide her sudden appearance from prying eyes.

''I'm going to meet with Gordon, you stay out here and keep watch,'' the Doctor said, before turning to Clarissa and pulled a key form his pocket. ''Here, this gets you back inside the TARDIS if you need to.''

''You mind giving me pepper-spray, too?'' Clarissa asked looking around the surroundings. ''I know I'm outside police department, but-''

''Here,'' the Doctor said giving Clarissa the pepper-spray. ''It's actually made from peppers grown on a farming planet formerly a weapons facility. So don't use it too much.''

''What happens if I use too much?'' Clarissa asked.

''Don't!'' the Doctor said as he walked out of the alley, leaving Clarissa with the TARDIS.

* * *

Getting inside the police department was easy with the psychic paper. The officer at the reception desk seemed mostly bored with his position he basically let the Doctor as soon as he showed his 'badge'. Walking inside there was another thing. The Doctor couldn't just walk out normally as normally he would walk around smiling, which would have stood out in this city. Not to mention he was un-escorted and an unknown face. That reminded the Doctor of the fact he hadn't even gotten a chance to see his new face since his last regeneration.

Eventually the Doctor managed to find Gordon's office by seeing Gordon enter it. He walked to the door and was about to knock it, until the lights went out and he heard a feint click inside, followed by a:

''Don't turn around, you're a good cop, one of the few.''

Gordon wasn't alone in there. He was with someone who had apparently sneaked in. The Doctor looked at the both ends of the hallway to make sure no one was watching and pulled out his stethoscope.

''What do you want?'' Gordon's voice asked nervously.

''Carmine Falcone bring his shipments of drugs in every week. Nobody takes him in. Why?'' mysterious voice asked, puzzeling the Doctor with his questions.

''He's paid up with the right people,'' was Gordon's shuttering response.

''What would it take to bring him down?'' was the mysterious voice's next question.

''Leverage in judge Faden,'' Gordon's voice said calmer, but still nervous, ''and a DA brave enough to prosecute.''

''Rachel Dawes,'' the mysterious voice said, shocking the Doctor by the mentioning of the Assistant DA's name.

''Who are you?'' Gordon finally asked from the voice, Doctor also waiting for its answer.

''Watch for my sign,'' the voice said and the Doctor's face grew even more puzzled.

''You're just one man?'' Gordon asked, his voice sounding much calmer now.

''Now were two.''

''We?'' Gordon asked and the Doctor heard noise outside the window. Whoever had been inside Gordon's office had left and was climbing out the fire-escape. Then Gordon ran out of the room and straight to the staircase. He was so much in a hurry that he didn't see the Doctor standing outside his office. It was lucky for the Time Lord, who left the building.

* * *

''Did you see that?!'' Clarissa asked coming to the Doctor as he walked out the Police Department. ''Some guy just jumped out of the roof to the next building.''

''You saw him?'' the Doctor asked taking her hand and walked her to the TARDIS. ''What did you see of him?''

''Not much, it was dark,'' Clarissa responded. ''But he was tall and muscular. And was wearing some kind of yellow harness and a ski-mask.''

The Doctor didn't respond to that as he put the TARDIS key to hole and let them inside. Once they were in side, he said what he was thinking.

* * *

**Author's notes: **What was the Doctor thinking about what he witnessed? What do you think about the situation? REVIEW!


	4. Bears and Rabbits

**Author's notes:** If you played the_ Batman Begins_ videogame for PS2 back in the day, I'm sure you'll recognize what Batman had done to the cops before the Doctor enters the docs here.

* * *

**Bears and Rabbits**

''Whatever that thing was, it must have jumped over the TARDIS,'' the Doctor said taking a look of screen on the console. ''She must have seen something.''

The footage shown on the screen showed a figure Clarissa had already described jumping from the other rooftop to another or at least trying. It didn't make it to the next roof and just fell to the fire-escape. After struggling to get on its feet, it went inside the building next to it.

''What was that?'' Clarissa asked looking at the Doctor.

''It could be anything,'' the Doctor said ''from an alien to another human. I heard it talking with Sergeant Gordon about Falcone's shipments and about taking him out.''

''So he was a vigilante?'' Clarissa asked.

''An amateur vigilante and not a good one obviously,'' the Doctor said turning to his companion. ''If he is going up against the likes of Falcone, he's not going to make out of it alive. But he had done some fantastic reconnaissance.''

''What?'' Clarissa asked.

''That vigilante knows that Rachel Dawes is the right DA to prosecute Falcone,'' The Doctor said, ''but that doesn't matter. What matters is that Falcone is the one bringing the contaminated flowers here and I'm going to destroy those flowers.''

* * *

Over the course of the next two days to the next shipment's arrival, the Doctor and Clarissa made their own reconnaissance work in getting to the flowers and keeping an eye on Rachel Dawes. By doing that, the Doctor managed to map out the docs of Gotham City harbor and Clarissa learned to walk around Gotham without getting into trouble. Actually when she was tailing Dawes, the Doctor was keeping an eye on her and giving the evil eye to everyone who seemed to look at Clarissa funny.

Eventually the big night of the next shipment came and while the Doctor had to go to docs to destroy it, Clarissa went on to shadow Rachel Dawes and keep her from dying. It also was the first they had to work separated in Gotham City and didn't have each other's backs. Clarissa was all alone protecting the Assistant DA and the Doctor was facing Falcone's hired help at the docs. A girl dressed in retro fashioned clothes and a man in black leather-jacket all on their own against the Gotham Underworld.

* * *

The Doctor walked into the docs at night time and saw police cars tilted and topped over. Scanning the surroundings with the sonic screwdriver, he found traces of sewer pluming been turned on full pressure, which had caused the pipes under the streets to shoot out hot steam in such a force that the cars had flown over.

''Impressive,'' the Doctor said admiring the work of whoever it was who had done it.

The deed had scared the corrupted police officers away and left the criminals exposed. Walking in to the shipment containers was now to some extent easier. All that the Doctor needed to do was to evade Falcone's thugs while going there.

Evading was actually easy or it just got harder the deeper into the Doctor managed to get. Falcone's hired help seemed to be only a very few people or they had skipped on coming to work. Or possibly someone was picking and them out, one by one. Either way, the Doctor managed to get himself to the cargo-ship and found the containers holding the shipments. Using the sonic screwdriver, he opened one of the containers and began to research the drugs in there.

The drugs were hidden in teddy bears and toy rabbits. Back in his third incarnation, the Doctor would have needed a whole lab to analyze the drugs to compare them to the flower he had brought from the Himalayas. Now he just needed to scan both the drugs with the sonic screwdriver and compare the readings from them to the flower's radiation. They matched.

''Fantastic,'' the Doctor said.

Finally he had found the remnants of Nightmare Child and was one more step closer to ending Daleks' weapon to harm anyone anymore. Now the Doctor just needed to find a way to destroy the drugs. He stepped out of the container to look for a way to, maybe dump them off the ship and to waters, only to be faced by six armed thugs pointing their guns at him. The Doctor's poker-face fell and he smiled at his own stupidity of not making sure the coast was clear.

''Take me to your leader,'' the Doctor said putting his hands up in the air. ''He must hear what I have to say about my findings.''

* * *

Detective Arnold Flass walked into the docs. Carmine Falcone's thugs were already unloading the shipment of drugs. The sight of a cop actually frightened the hired help and even more when he began to browse through the teddy bears and toy rabbits.

''What's this?'' Flass asked humored ripping the bears open and pulled out the small plastic bags filled with drugs. ''Heh-eh, continue.''

Flass threw the bears back to the pile and walked to the limo at the end of the line of containers. Carmine Falcone was sitting inside with someone else in a black leather-jacket.

''Detective Flass, you remember our dinner partner from Maroni's two nights ago?'' Falcone said pointing to the person sitting next to Flass in the limo.

''Yeah, he had that sweet looking date with him and they were sitting few tables from us,'' Flass said looking at the man in leatherjacket. ''She here too?''

''No, but my guys found him snooping around the ship's containers,'' Falcone said leaning closer, ''looking for a way to dispose my merchandise, claiming to be a doctor and that it's contaminated with some… space voodoo.''

Flass chuckled to this.

''Not that I'm actually buying any of it, but if his girl is also somewhere out there knowing he is here, I can't have him killed with someone alerting of disappearance here during my men being here too.''

Flass nodded and the Doctor gave both an evil eye.

''So, the bears go straight to the dealers?'' Flass asked changing the subject.

''And rabbits to our man in the Narrows,'' Falcone said.

''I hope that's to clarify that I'm telling the truth,'' the Doctor said, to which Falcone shook his head. ''Then why the hell are you splitting them up?''

''Not your problem, Doctor,'' Falcone said, hiding his nervously. ''And you, detective, shouldn't trouble yourself with the affairs of scary people.''

''Scarier than you?'' Flass asked.

Falcone didn't answer. There seemed to be some kind of commotion going on outside. Flass stepped outside and returned back quickly.

''Something's going on, you better bail.''

Flass left, leaving Falcone alone in the limo with the driver and the Doctor. Falcone stepped out to see what was going on while the Doctor attempted to make his escape from the mobster's hands. He had gotten his hands free and was opening the door as Falcone returned. Not even paying attention to the Doctor, he seemed more occupied in loading a shotgun.

''What the hell are you?'' Falcone muttered nervously as the Doctor opened the limo's door and jumped out, just in time to see whatever it was causing the commotion pulling Falcone through the limo's skylight and answering his question.

''I'm Batman!'' growled a huge figure in black with horns in its head and a flowing cape in its back.

It hit Falcone to forehead, knocking him out. Then looked at the distance and growled: ''Nice coat.''

Then it lifted up into the air with Falcone, vanishing into the darkness. As the Doctor got on his feet, looking up to where they had disappeared and then at a vagrant, possibly to whom the creature had spoken to.

''Thanks,'' the vagrant uttered, taken aback by the creature's hospitality.

* * *

Clarissa had been following Rachel Dawes for hours since she gotten out of work. Actually hour plus the time she had to wait for Dawes to get out of work. She had kept her distance not to stand out from the crowd, but now in the monorail, the crowd had turned into four, no, two people and them. It made Clarissa intimidated on how she could have protected Dawes and not to stand out anymore.

Eventually Dawes got off the monorail and as Clarissa was about to follow her, another passenger beamed after her. Clarissa kept tailing on and landing down the stairs to street level, she saw two thugs surrounding Dawes. Dawes hit the one behind her with her purse and pulled a tazer on the other one.

''Hold it!'' Dawes threatened at the other guy as Clarissa jumped down the stairs to assist her. As she landed, a black swarm of some kind attacked the thug.

The swarm moved slower as Clarissa got her vision clearer and she saw it was the vigilante that she had seen jumping from the roof of the police station. The ski-mask was changed to a horned mask and he had a cape that gave the vigilante the look of a bat. He beat the thug quickly in front of Clarissa's eyes and then turned to face Dawes. The thug she had had at tazer point had also seen the vigilante beating the other thug and ran away with Dawes thinking she had scared him off herself. As she turned around and saw the vigilante, she got frightened and shot him with her tazer. The tazer-wires hit the vigilante into the bicep, but thanks to the armor they didn't affect on him and he just pulled them out.

''Falcone sent them to kill you,'' the vigilante growled to Dawes.

''Why?'' Dawes asked shaken as Clarissa watched.

''You rambled his cage,'' was the vigilante's answer, before he threw some pictures to the ground near Clarissa's feet.

''What's this?'' Dawes asked, gesturing Clarissa to pick the pictures up and bring to her.

''Leverage.''

''For what?''

''To get things moving.''

''Who are you?'' Dawes asked as Clarissa brought the pictures to her.

''Someone like you, someone who rambles the cages,'' the vigilante growled as the two women looked at the pictures.

They showed an important looking middle aged man getting into a car with some blond.

''Judge Faden?'' Dawes said and looked back at the vigilante only to see him gone.

''So, blackmail?'' Clarissa asked and Dawes turned to her. ''I'm Clarissa, by the way.''

* * *

At the docs, Sergeant James Gordon joined his fellow officers and saw a bunch of thugs cuffed and a load of drugs, enough for conviction.

''Falcone's men,'' an officer told him.

''Does it matter?'' Gordon said frustrated. ''We couldn't connect him to this any way.''

''I wouldn't be so sure of that,'' the officer said, nodding his head towards a spotlight.

Falcone had been tied onto it and when looking up to clouded night sky where it was pointed up to, one could make up the symbol of a bat.

''We also have an eye witness,'' the officer said pointing to a man in black leather-jacket giving a statement to an officer. ''He says he's a doctor.''

* * *

**Author's notes:** Nightmare Child. That was the name of Davros' flagship during the Time War and it is what has contaminated the flowers Falcone uses for his drugs and League of Shadow to create Scarecrow's fear toxin. That is the reason for the Doctor is getting himself involved to these events.

And... REVIEW!


	5. Meetings

**Author's notes: **After that one short chapter, here, have a long one. And since no one complained on how slowly I have been writing, I might as well keep doing this slowly. No innuendo intended.

Also two interesting cameos in this chapter.

* * *

**Meetings**

For the last few hours, the Doctor had found out that the flowers he had followed to Gotham were the ones Falcone had shipped in and that James Gordon was the only good police officer in Gotham who actually listened to him. So far he had told the police sergeant that he was a travelling doctor with many doctorates, particularly in astronomy, biology, physics and history. Those four were how he had explained plausibly how he knew about the flowers and how they had been contaminated. True, some facts had been changed, but he had managed to convince Gordon of the danger they possessed.

He also had explained how he had followed their trail to Gotham from Himalayas and had arrived to Gotham three days earlier with his new lab assistant, Clarissa Oswin who he had given a day off tonight to keep her from getting into possible trouble the Doctor had himself gotten with Falcone.

''Thank you for your statement, Doctor Smith,'' Gordon said, referring the Doctor by the alias he had used in his UNIT days in his third incarnation, as he escorted him inside the GCPD. ''We will take as much effort as we can to find the rest of those flowers and... Oh no.''

They had been walking past the squad room where the Police Commissioner Loeb was addressing the other police officers with an early issue of Gotham Gazette's morning edition.

''This is un-acceptable,'' Loeb stated showing the front page, which had Falcone tied to a searchlight and headline 'Bat serves up Crime Boss'. ''Now, I don't care if this was a rivaling gangs, guardian angels or, the god-damn Salvation Army, I want them of the streets and my front page.''

''The said it was just one guy, or a creature,'' an officer said, making the other officers chuckle in amusement.

The Doctor understood the topic they were discussing was the vigilante he had initially mistaken for supernatural being before remembering it to be the vigilante that had jumped of the GCPD three days earlier.

''It was just some asshole in a costume,'' Loeb shot back, hiding his anger under a calm behavior. Gordon raised his hand to that. ''Yeah?''

''This guy delivered us the, city's most wanted crime lord,'' Gordon said, a bit nervously as the Doctor observed.

''Nobody, takes the law, into their own hands, in my city.'' Loeb told back to Gordon, not even caring about positivity of what 'the Batman' had done and just focused on the police force been ridiculed. ''Understand?''

''No, because apparently there a lot of people, who tend to break the law with their own hands. What have you recently done about them?'' The Doctor shot back with serious attitude. ''Nothing! But sure, waste all your resources and manpower, ON A MAN DRESSED AS A BAT!''

The Doctor's thrown opinion of Loeb's course of action silenced the entire squad room. Even Gordon looked shocked at the Doctor's serious look on his face. Then the Doctor turned away and walked out towards the exit doors. ''Fantastic police work!''

* * *

Commissioner Loeb didn't send anyone after the Doctor as he left. Not that he would even end up in a jail cell in this era. UNIT was active globally and one phone call with some keywords (Daleks, Cybermen, Zygons, Autons, Yeti, Great Intelligence etc.) and they would know who he was and be let free.

But now the Doctor was at an impasse. Finding the flowers was done now and their separate ways led to the dealers and Narrows. As the dealers, who would have been any number of people, were unable to be found quickly enough, Narrows was the best opinion for the next step to be taken.

And then there was this 'Batman' vigilante…

''Doctor!'' a voice called out and turning to its direction, the Doctor saw Clarissa running to him with… Rachel Dawes.

''What are you doing here?'' The Doctor asked, surprised of her arrival and her being accompanied by the Assistant DA. ''I thought I gave you… the night off?''

''You're her employer, Doctor Smith?'' Dawes shot questioning the Doctor, who nodded. ''Rachel Dawes, I'm the Assistant District Attorney.''

''Yes, I know who you are,'' the Doctor said, gaining a look from Dawes. ''I was at the city hall three days ago and overheard your conversation with Doctor Crane.''

''Ah, well,'' Dawes said, ''I heard about what happened at the docs and your lab assistant, who happened to be in my train ride, told me about you being there.''

''Before you begin to accuse me for being a part of Carmine Falcone's drug operation, I'm against it,'' the Doctor told very firmly showing the Assistant DA his flower from Himalayas. ''I was only there looking for these.''

''Yes, Clarissa told me about them,'' Dawes said reassuringly.

''About your findings about their contamination and assumptions of them been used to make Falcone's drugs,'' Clarissa said quickly, helping the Doctor out.

''Assumptions that I confirmed true tonight,'' the Doctor said, looking over his shoulder to the GCPD. ''Let's continue this somewhere else.''

* * *

The discussion was continued at a nearby restaurant, which had just opened its breakfast serving as it was dawn. The Doctor told Dawes about his past as the scientific advisor of UNIT as a base to his knowledge on the relevant issues connected to her investigations as the Assistant DA against Falcone. Dawes found everything the Doctor told, that which had been told believably, important to her investigations and with the evidence 'the Bat-Man' had provided her, she had enough evidence to bring Falcone down.

''Attempted manslaughter, bribery, illegal drug trafficking, and now, thanks to your witness account, neglecting a professional's warnings about the dangers of this drug,'' Dawes listed out charges against Falcone to the Doctor and Clarissa. ''And now with the help from that Bat-character, I even have the evidence and leverage to make judge Faden to convict him without fearing him to be bribed.''

''Happy to help,'' the Doctor replied smiling, while. ''By the way and while we're on the subject, what is your opinion on this Bat-Man?''

''So far I'm grateful for him providing me the evidence,'' Dawes answered as a waiter brought their supper. ''As much as you did with your testimony, Doctor Smith. The jury is still out for what he does next.''

''Stake and chips-''

''Right here,'' the Doctor said taking his order.

''A soufflé,-''

''That's mine,'' Clarissa said happily as she was served with her soufflé. ''Ah, I love these.''

''And a-'' the waiter was about to say.

''Yes thank you,'' Dawes said taking her order. ''I'm meeting with my boss at noon about this and I'd like to meet you afterwards for briefing.''

''Later today?'' The Doctor asked, to which the assistant DA nodded.

The Doctor smiled politely and nodded back before pulling out a calling card from his jacket and passed it to Dawes.

''Sure, here's the number to my phone box. Call us when you have spoken to your superior.''

* * *

It was the next evening when Rachel Dawes asked to see the Doctor and Clarissa again. This meeting was at fancier restaurant of the Royal Hotel at Gotham Diamond District. As it was a fancy restaurant they, the Doctor and Clarissa were forced to dress themselves more appropriately to the dress code.

To Clarissa it wasn't a problem. She had looked out the TARDIS wardrobe for something to wear and had found lots of fancy dresses from various different historical eras, before settling down to a white evening gown. To tone down the bright white contrast of it, Clarissa had thought to put a yellow star-like decoration on the gown's bust, but the Doctor had asked politely, and visibly sadly, for her not to.

''That belonged to a friend of mine,'' the Doctor said in a deep voice looking at the star. ''Someone who died.''

''Oh, sorry,'' Clarissa said taken aback and handing the star back. ''What happened to..?''

''He was on a ship that crashed,'' told the Doctor taking the star and turned away to put it away, ''all while I could only watch it happen as the TARDIS's console was damaged. I couldn't save him.''

''Okay,'' Clarissa replied and turned to look for something else to wear. They were only going to a meeting, not to a high school prom. ''What are you going to wear?''

''What's wrong with my jumper?''

Clarissa actually laughed to this.

''We're going to a fancy restaurant to meet the assistant DA,'' she said. ''I'm not going overdressed and you're not going dressed up like that. You'll start a riot-about.''

* * *

Eventually as they arrived to the Royal Hotel, the Doctor and Clarissa had picked their fancy clothes. What Clarissa had put on was now a dark red dress with a white overcoat. Doctor had changed his clothes mildly. All he had put on was a waist-coat and shirt under his leatherjacket. The look was to some extent the same as his previous incarnation. The reminder of that life made him look sad and depressed.

''Nice car'' a valet told to well-dressed man who had two dates with him in his Lamborghini, as the Doctor and Clarissa were entering the hotel restaurant.

''You should see my other one,'' the well-dressed man said picking up his dates and entered the hotel behind them.

The Doctor showed his psychic paper to the restaurant manager at the door, which showed him that he and Clarissa were guests of the assistant DA. They were told Dawes had not arrived yet, but they could wait in her table.

''You two know Rachel Dawes?'' the well-dressed man behind the Doctor and Clarissa asked.

''Yes,'' the Doctor answered. ''I'm the Doctor, and this is my lab assistant Clarissa.''

''Bruce Wayne,'' the well-dressed man introduced himself shaking the Doctor's hand. ''Rachel is my oldest friend, but I haven't seen her for seven years. Mind if I sit with you and wait for her?''

* * *

''Interesting work you do, Doctor,'' Bruce Wayne said after listening to a short description of the Doctor's 'work'. ''Thought I wouldn't call any work interesting as to I have my shares of Wayne Enterprises to live by.''

''Last surviving heir to the throne, I see'' the Doctor replied, ''not the first one I've met.''

''Bruce help me out here,'' a man in the next table asked. ''What is your opinion on this Batman?''

''Well, a guy who dresses himself as a bat,'' Wayne chuckled, ''would clearly have issues.''

''But he sent Falcone behind bars,'' a woman with curly blond hair and golden dress said.

''And now cops want to put him there. What does that tell you?''

''They are jealous,'' the woman replied.

''And thick,'' the Doctor said, making everyone look at him. ''What? It obvious, they did their job poorly and because of that, they are jealous, and thick, for someone who did their job better. But of course people like you see this Bat-Man as a menace because their life isn't in the area which is now changed with Falcone's arrest. Like the question of alien life, people want believe in them to exist as much this city's inhabitants want things to get better. But, as soon as they are looking at you straight in the face: 'NOPE! Can't see it.' There's a simple explanation to that: You're thick.''

Everyone kept their gaze on the Doctor for what he had just told. Only Clarissa, and the woman in golden dress for some reason, looked at him proudly. The silence was broken by the hotel manager who came to talk to Mr. Wayne.

''Sir, the pool is for decoration and your friends do not have any swimwear,'' was told by the manager and now everyone looked at the decoration pool where the two women Wayne had brought with him had taken a dip.

''Well, they're… Europeans,'' Wayne said pulling out his checkbook. ''No offence to you, Doctor, or your assistant.''

''I'm gonna have to ask you to leave,'' the manager said firmly, ''this is not a custom of money.''

''Look,'' Wayne said with a smug attitude, ''I'm buying this hotel and I'm making new rules, regarding the pool area.''

And then he left to pick his dates, who pulled him to the pool with him. As Wayne got himself up from the pull, he had some laughs with the women and they began to walk away, only to walk into Rachel Dawes entering the restaurant.

''Look who's in trouble now,'' Clarissa said amused watching Wayne explain himself to Dawes.

''I think the Batman deserves a medal,'' the woman said, leaving the table and smiled to the Doctor. ''Thank you, sweetie, for proving that point to everyone here.''

''What a lovely woman,'' the Doctor said watching the woman leaving as Dawes joined them. ''Good evening, counselor.''

* * *

The woman in golden dress exited the hotel and walked to an alley. Taking a look at her wrist watch, she counted to twelve and a blue police box materialized in front of her.

''River, don't you look lovely,'' the gray haired man said in Scottish accent exiting the box. ''Sorry if I'm late, the TARDIS kept for some reason refusing to land here.''

''Don't blame her, sweetie,'' River said calmly, ''and you're not late, Just early cause I saw you there already.''

''I'm there now?''

''Yes, meeting two different women at the same time,'' River said entering the TARDIS. ''Since the Royal Hotel is occupied, we might as well go to see those Singing Towers of Derilium you have been promising me.''

''Ah, not just quite yet,'' the Doctor said following her. ''I want to plan that out so that it will be as magnificent as… the future version of you said it was, or will be.''

''Well, you better. After promising to take me there so long, I think I'm already expecting too much of them.''

* * *

**Author' notes: **There, did you like that? I hope you did, now REVIEW to me what all you found interesting and what would you like to see next. Before we go to Arkham.


	6. Arkham Asylum

**Author's Notes:** This is a long chapter, because of the Doctor's memories being herel ike in my first story. They how ever are from the classic series, or most of them are and have the 1st, 3rd, 5th, 6th Doctors and the War Doctor.

* * *

** Arkham Asylum**

So, working with the assistant DA Rachel Dawes, the Doctor and Clarissa had managed to get closer finding the rest of Falcone's contaminated drugs. As Falcone was in lockup, Dawes had regularly visited him for questioning and had brought the Doctor with her for consultation. That was to make Falcone understand how big of a threat his drugs were as they were contaminated with the remnants of the Nightmare Child. Rachel had herself also began to call the drugs with that name, as there had been reports of people having fear fuelled symptoms here and there around Gotham and the ODs had the particular drug in their system. There were even some rumors that the Bat-Man had been seen drugged with it.

However their crusade against Falcone had been put on hold as suddenly the District Attorney Carl Finch had mysteriously disappeared. No one had seen him after the meeting the Doctor and Clarissa had been with him and Rachel at the Royal Hotel. The Doctor had agreed to help look for him on the second day of the disappearance. Nothing. Clarissa had even gone far enough to say that maybe the mob had taken him and he was now at the bottom of the river. Rachel didn't like the idea. On the third day of Finch's disappearance, Rachel accepted that maybe Clarissa was right and she was now the acting District Attorney of Gotham City until the next election in six months. That day also happened to be Bruce Wayne's birthday and no matter how bad image Wayne had given them at Royal, Rachel had decided to drop in at the Wayne Manor to drop her gift to him. With not exactly nothing better to do, the Doctor and Clarissa had decided to join her.

''You knew as children?'' the Doctor asked during the car ride.

''My mother was their house keeper,'' Rachel said, ''and there really wasn't many other children living in the next door.''

''Looks like we just drove past the next door,'' Clarissa said watching the passing scenery. ''Didn't you have any other friends besides him?''

''No, not before Bruce's parents died and we had to move to the city,'' Rachel told nostalgically. ''I sometimes think I should have kept in better touch with him, Bruce might be a better person then what you saw at Royal.''

''That was acting,'' the Doctor said plainly. ''He only looked like he was having fun, in reality he was just pretending.''

''What makes you say that?'' Rachel asked as they drove in front of the huge mansion with gardened trees surrounding it.

''His eyes didn't lie like his behavior did,'' the Doctor answered looking at the Wayne Manor. ''He is still mourning his parents deaths and this, fancy living or acting a party boy, isn't going to fix what he is feeling.''

''You know this from experience?'' Rachel asked as they exited the car and began to walk up the stairs to the front door.

''I have lost people in my life,'' the Doctor said looking down.

The door's opened to show oversized doorstep which led to even more stairs and to hallways to the lounges of the mansion. To greet them was an old strong built Englishman in servant's tuxedo, without the jacket, and a white apron.

''Miss Rachel,'' the man servant said delighted, ''it is good to see you again.''

''Hey, Alfred,'' Rachel said with same happiness and hugged the man. ''Oh, these are Doctor John Smith and his assistant Clarissa Oswin. They're consulting me on a case.''

''Hello,'' the Doctor said smiling and waving his hand with Clarissa.

''Doctor John Smith?'' Alfred asked mildly surprised. ''Brigadier Lethbridge-Stewart's scientific advisor, the Doctor John Smith, from UNIT?''

''You served with UNIT?'' the Doctor asked.

''In Burma, 1975-80, on some occasions under Lethbridge-Stewart,'' was Alfred's answer. ''I don't , however, recall ever seeing you with the Brigadier on that period.''

''We fought Daleks, Autons, Silurians, Zygons and Cybermen, not to mention the Master,'' the Doctor said with a firm attitude. ''And as the Brigadier himself said, it doesn't get more hostile than that. Oh, and I seemed to forget the Great Intelligence and the Yeti, battle where I met the Lethbridge-Stewart while he was still at the rank of Colonel.''

Alfred gave the Doctor some-what mysterious look before turning back to Rachel. ''Will you be staying for dinner?''

''We have to get,'' Rachel said apologizing while handing a small white box to Alfred. ''I only came to bring my gift.''

''Rachel?'' was heard from the top of the stairs and Bruce Wayne came down, wearing the kind of clothes which told them he had just gotten out of the bed.

''It's over three in the afternoon,'' Clarissa whispered to the Doctor.

Alfred turned to return up stairs and gave Rachel's gift to the birthday boy as they passed.

''Well, looks like someone's bee burning candle from the both ends,'' Rachel said as Bruce came down to them. ''Must have been some occasion.'' ''It's my birthday,'' Bruce said, to which both the Doctor and Clarissa smiled amused. ''Doctor, Clarissa.''

''For someone who acts like a child, you sure sleep over noon like an adult,'' the Doctor said, keeping the tone of his voice between complementing and insulting. ''You know how to live.''

''I'm sorry I can't come tonight'' Rachel said, breaking the verbal battle before it got the chance to start. ''I just came to give you your present.''

''You got better plans?'' Bruce asked offended.

''My boss has been missing for two days,'' Rachel said, stating it as a fact and not as an excuse.

''Which in this town means he's probably at the bottom of the river,'' Clarissa said, finishing Rachel's sentence.

Bruce seemed to try to apologize for his stupidity, but Rachel's mobile stopped him by ringing.

''Rachel Dawes,'' she answered to the phone. ''Who authorized that? Get Crane down there right away, don't take no for an answer, I'm bringing Doctor Smith to get our own assessment and have it for the judges by morning.''

''You're bringing me to what?'' the Doctor asked as Rachel closed her phone.

''Falcone, Crane moved him to Arkham Asylum for suicide watch,'' Rachel told him.

''You're going to Arkham now?'' Bruce asked, with his voice noticeably different than just before. ''It's in the Narrows, Rachel.''

''Well thank you for being concerned about us too,'' Clarissa said.

''Enjoy your party, Bruce,'' Rachel told him as a goodbye. ''Some of us have work to do.''

* * *

Driving in the Narrows, the Doctor and Clarissa understood why Bruce Wayne had been so concerned about their safety. It was not the nicest neighborhoods in Gotham. It could have been said, that as in other parts of the city its nature was hidden, in Narrows everything bad was shown and exposed to the bare eye. Arkham Asylum however, was closed from the rest of the island with walls and barbwire. The whole place seemed like it was very old and just updated recently to modern age. It reminded the Doctor of the medieval castle Sontaran Lynx had tried to modernize and he had himself stopped during his third incarnation with Sarah-Jane.

Nostalgia seemed to make him feel better, until the Doctor's memories eventually returned to Time War and… No he was here and now. And the Time War wasn't over until he had destroyed the every last, single traces of Daleks and the Nightmare Child.

* * *

Falcone was being held in a cell, strapped to bed and uttering 'scarecrow' over and over again. The Doctor, Rachel and Clarissa observed the mobster from the hallway in the other side of the glass while waiting for Dr. Crane to arrive.

''Miss Dawes and two others, this is most irregular,'' Crane said as he arrived to them.'' I have nothing further to add to the report I filed with the judge.''

''These two are Doctor Smith and his assistant miss Oswin,'' Rachel told Crane as the Doctor and Clarissa nodded to him. ''We have questions about your report.''

Crane looked at the Doctor and Clarissa before asking: ''Such as?''

''How convenient is it for a 52-year-old man who has no history of mental illness to suddenly have a complete psychotic breakdown,'' Rachel asked with a firm attitude, adding,'' just when he's about to be indicted?''

''Zero,'' the Doctor said pointing his hand at Falcone. ''But there he is muttering nonsense. Now, why and how could that be?''

''Well, as you can see for yourself,'' Crane said pointing his answer to both Rachel and the Doctor, ''there is nothing "convenient" about his symptoms.''

'' Hey, why does he keep saying "scarecrow" over and over again?'' Clarissa asked suddenly.

''Patients suffering delusional episodes often focus their paranoia on an external tormentor. Usually one conforming to Jungian archetypes,'' Crane answered speaking with words only a professional, and the Doctor could understand. ''In this case, a scarecrow.''

''You mean you had people dress up a scarecrows and then put them to torment Falcone?'' The Doctor asked disgusted, remembering the experience he had had when he was forced to regenerate from his second incarnation to third.

''Outside, he was a giant,'' Crane said calmly. ''In here, only the mind can grant you power.''

'' And you enjoy the reversal?'' Clarissa asked with the same attitude as the Doctor.

''I respect the mind's power over the body,'' was Crane's answer. ''It's why I do what I do.''

''I do what I do to keep thugs like Falcone behind bars, not in therapy,'' Rachel said moving to elevator. ''Doctor Smith is going to reevaluate your diagnosis and check Falcone's blood work. I'm going to find out what you gave to him.''

''Right now?'' Crane asked as all four were in the elevator.

''Yes,'' Rachel said nodding her head towards the Doctor, ''that is why I brought him here.''

''As you wish,'' Crane said pressing a button on the panel and turned a key in the lock.

* * *

To everyone's surprise, the elevator took them down instead of up, to the file room. They stepped out to a dark lit hallway that took them to a balcony.

''This is where we make the medicine,'' Crane said walking ahead and showed them a large basement room, where men in red jumpsuits were dumping some kind of liquid to the busted pipe where the water was running. ''Perhaps you all should have some, clear your head.''

That was when the Doctor knew they were all in danger. He grabbed both women's hands and told them: ''Run!''

They ran back to the elevator and tried to make it go up. Then the Doctor remembered Crane had used a key for them to come down there. He was about to pull out the sonic screwdriver and use it to the panel when the door opened and they all saw Crane, wearing a scarecrow mask. That was the last any of them saw before Crane gassed them with, as the Doctor assumed, Nightmare Child.

* * *

_''Come, Susan! We have to hurry!'' The Doctor told his granddaughter. ''If get to the repair shop, we might find a TARDIS to escape.''_

_ ''But, Grandfather, it would brand us criminals and fugitives,'' Susan said as they ran. ''No one is meant to leave Gallifrey and go involve themselves with the issues of outside universe.''_

_ ''I know this, child,'' the Doctor said opening the doors to repair shop. ''But we can't stay here any longer. Gallifrey and its laws have changed to worse.'' _

_''I suppose you're right,'' Susan said as they entered to the repair shop. ''But where would we go?'' _

_''Oh, my child,'' the Doctor said, ''it is a vast universe and we have all the time in the world.''_

_ They went around the storage and found three TARDIS' laying around in their default modes._

_ ''Quickly, Susan, get in one of them,'' the Doctor told his granddaughter and she obeyed entering one of the TARDIS'. _

_The Doctor was about to follow her, but suddenly heard someone calling out to him._

_ ''Doctor, Doctor…'' _

_''Yes?'' The Doctor asked turning to the direction of the voice and saw a young Time Lady approaching him. ''What is it? What do you want?''_

_ ''Sorry, but you are about to make a big mistake,'' the young Time Lady said. The Doctor felt fear. Was this young Time Lady there to tell him off and alert the guards of what he was doing? _

_''Don't steal that one, steal this one,'' the young Time Lady said leaning to the other TARDIS next to her. ''The navigation system is a bit dodgy, you'll have much more fun.'' _

_''Thank you,'' the Doctor said confused of the young Time Lady's actions, but relieved that she hadn't done him ill. ''Come out, Susan. I found the right one.'' _

* * *

_''Courage is never about not being frightened, you know,'' the Doctor told to the thal he was prisoned with by the Daleks._

_ ''Oh,'' the thal said. ''What is it then?''_

_ ''It is about being afraid and doing what you have to do any way,'' the Doctor answered nodding his head. ''Just as you did.'' _

* * *

_''But you will not enjoy the victory,'' the Cyberman said raising its gun arm,''I shall kill you now, Doctor.''_

_ But before it could, Tegan took a hold of it and gave the Doctor a chance to fight it. Twisting the Cyberman's gun arm against its own chest and making it fire. That was all needed to destroy it. Sparks flew from the Cyberman as it was no more operational._

_ ''Look out!'' Nyssa yelled as the Doctor was fixing the TARDIS console. Another Cyberman was approaching them. _

_''I must save Adric!'' the Doctor yelled back. If he could fix the damage the Cybermen had done, there would still be a chance to save Adric from the falling spaceliner. Nyssa took the fallen Cyberman's gun-arm and fired it at the other one._

_ ''Look!'' Tegan said pointing at the screen on the wall showing the ship Adric was on._

_ Nyssa looked at it, the Doctor too. They all could nothing but watch as it exploded, destroying everything and everyone on board. Tegan and Nyssa hugged as the Doctor turned away speechless. _

_''Adric?'' he heard Tegan say. ''DOCTOR!''_

_ But the Doctor could not speak, he was at loss for words and could only see Nyssa and Tegan holding each other in tears. Adric was dead._

* * *

_ Peri's hair was shaven of from her but the words and the voice that came from her mouth weren't her. It wasn't Peri anymore. Then the Kroatin assassin barged to the room where Peri was and set it to explode, killing everyone. _

_''You… killed Peri? the Doctor said shocked of what he had been shown._

_ ''We had to act!'' Madam President said. ''With the Discovery that Krotia had made course the force of natural evolution throughout the universe would be effected.'' _

_''But Peri died, Doctor,'' The Valeyard spoke,'' because you abandoned her. We had to end her life because your negligence had made it impossible for her to live.'' _

_''Lies!'' The Doctor said in despair of his deceased companion. ''There is something else going on here. The High Council had no right to order Peri's… or anyone else's death!''_

* * *

_What had he done? He stood in ruins of Gallifrey, before it could break apart and spread to ashes and stardust. He had ended the War, but at the cost of being now the last of his kind. Even this incarnation had aged rapidly from the young man he had been to an old man. And for what? _

_''What I did,'' he tried to convince himself, ''I did without choice.''_

_ ''I know,'' a voice, maybe his conscience, said. _

_''In the Name of Peace and Sanity,'' He continued._

_ ''But not in the Name of the Doctor!'' the voice said again, bitter._

_ He turned around just in time to see a tall figure walking away from him, carrying away… Clarissa?_

* * *

''You want the cops here?''

The Doctor regained his consciousness and remembered where he was. Crane and some armed, pointing their guns at ceiling, were standing over him and the still drugged Clarissa and Rachel. The Doctor had apparently woken up sooner thanks to his Time Lord metabolism.

''At this point they can't stop us. But the Batman,'' Crane said putting pressure on the vigilante's name, ''has the talent for disruption, hold him of until they arrive. They'll take care of him.''

''What about them?''

''Ah, they don't have long. I gave them all a concentrated dose,'' Crane told his men half calm, half exited. ''The mind can only take that much.''

''Is it true what they say about him?'' The Doctor listened to thugs ask. ''Can he really fly?''

''I heard he can disappear.''

''Well, we'll find out,'' Crane said looking around in the dark basement room.

Suddenly one of the thugs disappeared, Batman had taken him. The other thugs panicked as even more disappeared and in the commotion, the Doctor raised on his feet. He used his Venusian Aikido to take out one of the thugs in attempt to help Batman, but was soon discovered.

''What the Hell!?'' one of the thugs said as he saw the Doctor. ''Hey Doc, I thought you said this dose was lethal!?''

''LETHAL TO HUMANS MAYBE!'' The Doctor yelled intimidatingly and pointed his sonic screwdriver at the thug, breaking it to pieces.

At this point Batman had taken out every other thug in the room and after taking out the last one, he barged at Crane. The Doctor saw as Crane tried to poison Batman, who stroke away Crane's weapon arm, pulled the scarecrow-mask off and gassed him with his own poison.

''Taste of your own medicine, doctor,'' the vigilante growled at him, while the Doctor took a look Rachel and Clarissa. ''What have you been doing here? CRANE! WHO ARE YOU WORKING FOR!?''

''Ra's…'' the Doctor heard Crane's response. ''Ra's al Ghul…''

''Ra's al Ghul is dead!'' Batman barked back to Crane. ''WHO ARE YOU WORKING FOR!? CRANE!?''

''Doctor Crane isn't here right now, but if you'd like to make an appointment…'' Crane couldn't say more as Batman hit his head against the wall and then came to the Doctor.

''Doctor Smith, I presume.''

''Batman, I presume,'' the Doctor said rising to face the vigilante. ''They have less than an hour before their minds are gone completely.''

''We need to get them to my cave,'' Batman told him. ''I have antidote.''

''What?'' The Doctor asked. ''How?''

''I was poisoned with this toxin earlier this week and I had someone make an antidote to cure me,'' was Batman's answer. ''I also asked them to make more.''

''Fair enough,'' The Doctor said taking Clarissa on his arms and nodded his head towards Rachel. ''You take her; we need to get them both to-''

''BATMAN! THIS IS THE POLICE!'' was suddenly heard from outside the building. The GCPD had arrived as the Doctor remembered Crane ordering his thugs to call them. ''LAY DOWN YOUR WEAPONS AND COME OUT WITH YOUR HANDS UP!''

''Fantastic.''

* * *

**Author's notes:**Review about the Story are welcome. This is a long one so I want as much criticism. Also Alfred worked with the UNIT back in the classic era. What should I do with this fact.

By the way, TRUE STORY: Yesterday I saw sick and weak. As I laid on my bed, I opened Facebook on my phone and saw the link to _Night of the Doctor_. As I opened it and saw Paul McGann as the 8th Doctor I gained the strength to get out of bed. I felt as if the Doctor had healed. This was a true story I had to share with you all.


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